Changing atmospheric conditions, including above all the deepening extreme weather phenomena, are increasing from year to year. This, in consequence, causes an increase in the incidence of low outflows. The study compares low water levels for two catchments: Biała Woda and Czarna Woda, and phosphorus and nitrogen load using the Nutrient Delivery Ratio (NDR) model in InVEST software. The objective of the NDR is to map nutrient sources from catchment area and transfer to the river bed. The nutrient loads (nitrogen and phosphorus) spread across the landscape are determined based on a land use (LULC) map and associated loading rates described in literature. The studies have shown that low water levels have been more common recently and pose the greatest threat to the biological life in the aquatic ecosystems. The structure of land use is also of great importance, with a significant impact on the runoff and nitrogen and phosphorus load. Phosphorus and runoff from surface sources to the water of Biała Woda and Czarna Woda catchments area has been reduced in forested areas. Only higher run-offs are observed in the residential buildings zone. The nitrogen load was also greater in the lower (estuary) parts of both catchments, where residential buildings dominate.